Search Results - "Feher, Victoria"

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation by Miao, Yinglong, Feher, Victoria A, McCammon, J. Andrew

“…A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By…”
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Emerging Computational Methods for the Rational Discovery of Allosteric Drugs by Wagner, Jeffrey R, Lee, Christopher T, Durrant, Jacob D, Malmstrom, Robert D, Feher, Victoria A, Amaro, Rommie E

“…Allosteric drug development holds promise for delivering medicines that are more selective and less toxic than those that target orthosteric sites. To date,…”
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Computational approaches to mapping allosteric pathways by Feher, Victoria A, Durrant, Jacob D, Van Wart, Adam T, Amaro, Rommie E

“…•Advances in computational methods for allosteric pathways are reviewed.•New methods are able to replicate many but not all experimental results.•Each method…”
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D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies by Gaieb, Zied, Liu, Shuai, Gathiaka, Symon, Chiu, Michael, Yang, Huanwang, Shao, Chenghua, Feher, Victoria A., Walters, W. Patrick, Kuhn, Bernd, Rudolph, Markus G., Burley, Stephen K., Gilson, Michael K., Amaro, Rommie E.

“…The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures…”
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D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions by Gathiaka, Symon, Liu, Shuai, Chiu, Michael, Yang, Huanwang, Stuckey, Jeanne A., Kang, You Na, Delproposto, Jim, Kubish, Ginger, Dunbar, James B., Carlson, Heather A., Burley, Stephen K., Walters, W. Patrick, Amaro, Rommie E., Feher, Victoria A., Gilson, Michael K.

“…The Drug Design Data Resource (D3R) ran Grand Challenge 2015 between September 2015 and February 2016. Two targets served as the framework to test community…”
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Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A by Schiffer, Jamie M., Feher, Victoria A., Malmstrom, Robert D., Sida, Roxana, Amaro, Rommie E.

“…Proteins commonly sample a number of conformational states to carry out their biological function, often requiring transitions from the ground state to…”
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Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant by Feher, Victoria A., Schiffer, Jamie M., Mermelstein, Daniel J., Mih, Nathan, Pierce, Levi C.T., McCammon, J. Andrew, Amaro, Rommie E.

“…The atomic-level mechanisms that coordinate ligand release from protein pockets are only known for a handful of proteins. Here, we report results from…”
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Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking by Wagner, Jeffrey R., Churas, Christopher P., Liu, Shuai, Swift, Robert V., Chiu, Michael, Shao, Chenghua, Feher, Victoria A., Burley, Stephen K., Gilson, Michael K., Amaro, Rommie E.

“…Docking calculations can accelerate drug discovery by predicting the bound poses of ligands for a targeted protein. However, it is not clear which docking…”
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A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins by Feher, Victoria A, Randall, Arlo, Baldi, Pierre, Bush, Robin M, de la Maza, Luis M, Amaro, Rommie E

“…Chlamydia trachomatis is the most prevalent cause of bacterial sexually transmitted diseases and the leading cause of preventable blindness worldwide. Global…”
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Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop by Adams, Paul D., Aertgeerts, Kathleen, Bauer, Cary, Bell, Jeffrey A., Berman, Helen M., Bhat, Talapady N., Blaney, Jeff M., Bolton, Evan, Bricogne, Gerard, Brown, David, Burley, Stephen K., Case, David A., Clark, Kirk L., Darden, Tom, Emsley, Paul, Feher, Victoria A., Feng, Zukang, Groom, Colin R., Harris, Seth F., Hendle, Jorg, Holder, Thomas, Joachimiak, Andrzej, Kleywegt, Gerard J., Krojer, Tobias, Marcotrigiano, Joseph, Mark, Alan E., Markley, John L., Miller, Matthew, Minor, Wladek, Montelione, Gaetano T., Murshudov, Garib, Nakagawa, Atsushi, Nakamura, Haruki, Nicholls, Anthony, Nicklaus, Marc, Nolte, Robert T., Padyana, Anil K., Peishoff, Catherine E., Pieniazek, Susan, Read, Randy J., Shao, Chenghua, Sheriff, Steven, Smart, Oliver, Soisson, Stephen, Spurlino, John, Stouch, Terry, Svobodova, Radka, Tempel, Wolfram, Terwilliger, Thomas C., Tronrud, Dale, Velankar, Sameer, Ward, Suzanna C., Warren, Gregory L., Westbrook, John D., Williams, Pamela, Yang, Huanwang, Young, Jasmine

“…Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning…”
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In Vitro and In Vivo Inhibition of the Mycobacterium tuberculosis Phosphopantetheinyl Transferase PptT by Amidinoureas by Ottavi, Samantha, Scarry, Sarah M, Mosior, John, Ling, Yan, Roberts, Julia, Singh, Amrita, Zhang, David, Goullieux, Laurent, Roubert, Christine, Bacqué, Eric, Lagiakos, H. Rachel, Vendome, Jeremie, Moraca, Francesca, Li, Kelin, Perkowski, Andrew J, Ramesh, Remya, Bowler, Matthew M, Tracy, William, Feher, Victoria A, Sacchettini, James C, Gold, Ben S, Nathan, Carl F, Aubé, Jeffrey

“…A newly validated target for tuberculosis treatment is phosphopantetheinyl transferase, an essential enzyme that plays a critical role in the biosynthesis of…”
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The Role of Bridging Water and Hydrogen Bonding as Key Determinants of Noncovalent Protein–Carbohydrate Recognition by Ruvinsky, Anatoly M., Aloni, Ishita, Cappel, Daniel, Higgs, Chris, Marshall, Kyle, Rotkiewicz, Piotr, Repasky, Matt, Feher, Victoria A., Feyfant, Eric, Hessler, Gerhard, Matter, Hans

“…Mechanisms of protein–carbohydrate recognition attract a lot of interest due to their roles in various cellular processes and metabolism disorders. We have…”
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Molecular docking to flexible targets by Sørensen, Jesper, Demir, Özlem, Swift, Robert V, Feher, Victoria A, Amaro, Rommie E

“…It is widely accepted that protein receptors exist as an ensemble of conformations in solution. How best to incorporate receptor flexibility into virtual…”
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Structural characterisation of Tpx from Yersinia pseudotuberculosis reveals insights into the binding of salicylidene acylhydrazide compounds by Gabrielsen, Mads, Beckham, Katherine S H, Feher, Victoria A, Zetterström, Caroline E, Wang, Dai, Müller, Sylke, Elofsson, Mikael, Amaro, Rommie E, Byron, Olwyn, Roe, Andrew J

“…Thiol peroxidase, Tpx, has been shown to be a target protein of the salicylidene acylhydrazide class of antivirulence compounds. In this study we present the…”
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Structure-based design and SAR development of 5,6-dihydroimidazolo[1,5-f]pteridine derivatives as novel Polo-like kinase-1 inhibitors by Kiryanov, Andre, Natala, Srinivasa, Jones, Benjamin, McBride, Christopher, Feher, Victoria, Lam, Betty, Liu, Yan, Honda, Kouhei, Uchiyama, Noriko, Kawamoto, Tomohiro, Hikichi, Yuichi, Zhang, Lilly, Hosfield, David, Skene, Robert, Zou, Hua, Stafford, Jeffrey, Cao, Xiaodong, Ichikawa, Takashi

“…[Display omitted] Using structure-based drug design, we identified a novel series of 5,6-dihydroimidazolo[1,5-f]pteridine PLK1 inhibitors. Rational…”
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Millisecond-timescale motions contribute to the function of the bacterial response regulator protein Spo0F by Cavanagh, John, Feher, Victoria A

“…Protein backbones and side chains display varying degrees of flexibility, which allows many slightly different but related conformational substates to occur…”
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Structure-based design and synthesis of pyrrole derivatives as MEK inhibitors by Wallace, Michael B., Adams, Mark E., Kanouni, Toufike, Mol, Clifford D., Dougan, Douglas R., Feher, Victoria A., O’Connell, Shawn M., Shi, Lihong, Halkowycz, Petro, Dong, Qing

“…A series of potent pyrrole-based inhibitors of MEK kinase was designed and synthesized. Structural properties and biological activities are described. A novel…”
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Discovery of TAK-960: An orally available small molecule inhibitor of polo-like kinase 1 (PLK1) by Nie, Zhe, Feher, Victoria, Natala, Srinivasa, McBride, Christopher, Kiryanov, Andre, Jones, Benjamin, Lam, Betty, Liu, Yan, Kaldor, Stephen, Stafford, Jeffrey, Hikami, Kouki, Uchiyama, Noriko, Kawamoto, Tomohiro, Hikichi, Yuichi, Matsumoto, Shin-ichi, Amano, Nobuyuki, Zhang, Lilly, Hosfield, David, Skene, Robert, Zou, Hua, Cao, Xiaodong, Ichikawa, Takashi

“…Using structure-based drug design, we identified and optimized a novel series of pyrimidodiazepinone PLK1 inhibitors resulting in the selection of the…”
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Structure-Based Design, Synthesis, and Antimicrobial Activity of Indazole-Derived SAH/MTA Nucleosidase Inhibitors by Li, Xiaoming, Chu, Sam, Feher, Victoria A, Khalili, Mitra, Nie, Zhe, Margosiak, Stephen, Nikulin, Victor, Levin, James, Sprankle, Kelly G, Tedder, Martina E, Almassy, Robert, Appelt, Krzysztof, Yager, Kraig M

“…The structure-based design, synthesis, and biological activity of a novel indazole-containing inhibitor series for S-adenosyl homocysteine/methylthioadenosine…”
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Computation-Guided Discovery of Influenza Endonuclease Inhibitors by Chen, Eric, Swift, Robert V, Alderson, Nazilla, Feher, Victoria A, Feng, Gen-Sheng, Amaro, Rommie E

“…Influenza is a global human health threat, and there is an immediate need for new antiviral therapies to circumvent the limitations of vaccination and current…”
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